Carr was previously associate director at the agency, where she has worked since 2010.
Further changes within the agency mean that she will have the support of Carl Thomson, who is promoted from associate director to director, as she oversees a team of 20 staff.
Discussing her new appointment Carr said: "I have worked in private, public and third sectors in the past and this coupled with my in-depth awareness of The Whitehouse Consultancy will enable me to fulfil my new role."
Whitehouse denied that he was stepping back from the agency’s affairs following his appointment, but said: "My role has changed from one that is dealing with details of running the business to more ambassadorial and strategic involvement."
He revealed that health, environment and education policy development are growth sectors where the company is investing in staff.
He added: "We need a new structure to cope with further growth and take Whitehouse to the next level. We are delighted that Emma is stepping up to the plate and have every confidence for the future."
Carr previously worked for Social Market Foundation, Bupa, The Commission for Social Care Inspection and Consumer Focus.